TM4SF5

transmembrane 4 L six family member 5

Basic information

Region (hg38): 17:4771884-4783213

Links

ENSG00000142484 ∙ NCBI:9032 ∙ OMIM:604657 ∙ HGNC:11857 ∙ Uniprot:O14894 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TM4SF5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TM4SF5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in TM4SF5

This is a list of pathogenic ClinVar variants found in the TM4SF5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-4772083-T-C		not specified	Uncertain significance (Jun 29, 2023)
17-4780813-G-A		not specified	Uncertain significance (Apr 18, 2023)
17-4780817-G-A		not specified	Uncertain significance (Jan 26, 2022)
17-4782545-G-A		not specified	Uncertain significance (May 20, 2024)
17-4782573-C-A		not specified	Uncertain significance (Jun 05, 2023)
17-4782605-A-G		not specified	Uncertain significance (Aug 02, 2021)
17-4782629-G-A		not specified	Uncertain significance (Mar 02, 2023)
17-4782922-A-C		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TM4SF5	protein_coding	protein_coding	ENST00000270560	5	11328

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00792	0.935	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.795	108	134	0.807	0.00000857	1251
Missense in Polyphen		51	57.016	0.89449		579
Synonymous	0.522	54	59.1	0.914	0.00000415	431
Loss of Function	1.64	5	10.8	0.461	6.47e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000297	0.000290
Middle Eastern	0.000544	0.000544
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.682
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.229
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.108

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tm4sf5

Zebrafish Information Network

• Gene name: tm4sf5
• Affected structure: fast muscle cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Cellular component: integral component of plasma membrane